Hola,
No se pueden eliminar los Automatic Tie Points (los que se generan al paso 1 de procesamiento) pero los puntos de de la nube de puntos que se genera al paso 2 si se pueden eliminar.
Para la generacion de las curvas de nivel se toman en cuenta los puntos que se generan al paso 2, asi que no importa si los Automatic Tie Points de paso 1 incluyen los arboles.
Aqui puedes ver mas informacion sobre como generar curvas de nivel solamente del terreno:
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